The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region

The function of Arctic soil ecosystems is crucially important for the global climate, and nitrogen (N) is the major limiting nutrient in these environments. This study assessed the effects of changes in nitrogen content on archaeal community diversity and composition in the Arctic lake area (London Island, Svalbard). A total of 16S rRNA genes were sequenced to investigate archaeal community composition. First, the soil samples and sediment samples were significantly different for the geochemical properties and archaeal community composition. Thaumarchaeota was an abundant phylum in the nine soil samples. Moreover, Euryarchaeota, Woesearchaeota, and Bathyarchaeota were significantly abundant phyla in the three sediment samples. Second, it was found that the surface runoff caused by the thawing of frozen soil and snow changed the geochemical properties of soils. Then, changes in geochemical properties affected the archaeal community composition in the soils. Moreover, a distance-based redundancy analysis revealed that NH4+–N (p < 0.05) and water content were the most significant factors that correlated with the archaeal community composition. Our study suggests that nitrogen content plays an important role in soil archaeal communities. Moreover, archaea play an important role in the carbon and nitrogen cycle in the Arctic lake area.

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Potential Oxygen Consumption and Community Composition of Sediment Bacteria in a Seasonally Hypoxic Enclosed Bay

10.21203/rs.3.rs-350980/v1 ◽

2021 ◽

Author(s):

Fumiaki Mori ◽

Yu Umezawa ◽

Ruji Kondo ◽

Gregory N. Nishihara ◽

Minoru Wada

Keyword(s):

Oxygen Consumption ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sediment Surface ◽

Tetrazolium Chloride ◽

Sediment Samples ◽

Potential Oxygen

Abstract The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a notable shift in the bacterial community composition before and after the INT assay incubation. Within the bacterial community that was predominated by the ASVs closely related to Woeseia (Woeseiaceae, Gammaproteobacteria), the relative abundance of ASVs affiliated with Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, increased markedly in the summer samples. These findings have implications not only for the group of bacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

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Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon

Archaea ◽

10.1155/2006/710190 ◽

2006 ◽

Vol 2 (1) ◽

pp. 31-38 ◽

Cited By ~ 24

Author(s):

Melissa M. Kendall ◽

David R. Boone

Keyword(s):

Marine Sediments ◽

Enrichment Culture ◽

Sequence Similarity ◽

Pcr Amplification ◽

Archaeal Community ◽

Rrna Genes ◽

Rrna Gene ◽

Single Strain ◽

Sediment Samples ◽

Hydrate Ridge

Little is known about the methanogenic degradation of acetate, the fate of molecular hydrogen and formate or the ability of methanogens to grow and produce methane in cold, anoxic marine sediments. The microbes that produce methane were examined in permanently cold, anoxic marine sediments at Hydrate Ridge (44°35' N, 125°10' W, depth 800 m). Sediment samples (15 to 35 cm deep) were collected from areas of active methane ebullition or areas where methane hydrates occurred. The samples were diluted into enrichment medium with formate, acetate or trimethylamine as catabolic substrate. After 2 years of incubation at 4 °C to 15 °C, enrichment cultures produced methane. PCR amplification and sequencing of the rRNA genes from the highest dilutions with growth suggested that each enrichment culture contained a single strain of methanogen. The level of sequence similarity (91 to 98%) to previously characterized prokaryotes suggested that these methanogens belonged to novel genera or species within the orders Methanomicrobiales and Methanosarcinales. Analysis of the 16S rRNA gene libraries from DNA extracted directly from the sediment samples revealed phylotypes that were either distantly related to cultivated methanogens or possible anaerobic methane oxidizers related to the ANME-1 and ANME-2 groups of the Archaea. However, no methanogenic sequences were detected, suggesting that methanogens represented only a small proportion of the archaeal community.

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Microbial diversity and hydrocarbon depletion in low and high diesel-polluted soil samples from Keller Peninsula, South Shetland Islands

Antarctic Science ◽

10.1017/s0954102014000728 ◽

2014 ◽

Vol 27 (3) ◽

pp. 263-273 ◽

Cited By ~ 16

Author(s):

Juliano C. Cury ◽

Diogo A. Jurelevicius ◽

Helena D.M. Villela ◽

Hugo E. Jesus ◽

Raquel S. Peixoto ◽

...

Keyword(s):

Action Plan ◽

Archaeal Community ◽

Small Subunit ◽

Soil Samples ◽

Rrna Genes ◽

South Shetland Islands ◽

Small Subunit Rrna ◽

High Concentration ◽

Antarctic Soils ◽

Eukaryotic Diversity

AbstractThe bioremediation of Antarctic soils is a challenge due to the harsh conditions found in this environment. To characterize better the effect of total petroleum hydrocarbon (TPH) concentrations on bacterial, archaeal and microeukaryotic communities in low (LC) and high (HC) hydrocarbon-contaminated soil samples from the Maritime Antarctic clone libraries (small-subunit rRNA genes) were constructed. The results showed that a high concentration of hydrocarbons resulted in a decrease in bacterial and eukaryotic diversity; however, no effect of the TPH concentration was observed for the archaeal community. The HC soil samples demonstrated a high relative abundance of bacterial operational taxonomic units (OTUs) affiliated with unclassified group TM7 and eukaryotic OTUs affiliated with unclassified fungi from Pezizomycotina subphyla. Chemical analyses of the LC and HC soil samples revealed the presence of negligible amounts of nitrogen, thereby justifying the use of biostimulation to remediate these Antarctic soils. Microcosm experiments showed that the application of fertilizers led to an increase of up to 27.8% in the TPH degradation values. The data presented here constitute the first step towards developing the best method to deploy bioremediation in Antarctic soils and provide information to indicate an appropriate action plan for immediate use in the case of new accidents.

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Chemical Properties of Heavy Metal-Contaminated Soils from a Korean Military Shooting Range: Evaluation of Pb Sources Using Pb Isotope Ratios

Applied Sciences ◽

10.3390/app11157099 ◽

2021 ◽

Vol 11 (15) ◽

pp. 7099

Author(s):

Inkyeong Moon ◽

Honghyun Kim ◽

Sangjo Jeong ◽

Hyungjin Choi ◽

Jungtae Park ◽

...

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Contaminated Soils ◽

Management Strategies ◽

Chemical Properties ◽

Heavy Metal Concentration ◽

Soil Samples ◽

Shooting Range ◽

Geochemical Properties ◽

Mineral Phases

In this study, the geochemical properties of heavy metal-contaminated soils from a Korean military shooting range were analyzed. The chemical behavior of heavy metals was determined by analyzing the soil pH, heavy metal concentration, mineral composition, and Pb isotopes. In total, 24 soil samples were collected from a Korean military shooting range. The soil samples consist of quartz, albite, microcline, muscovite/illite, kaolinite, chlorite, and calcite. Lead minerals, such as hydrocerussite and anglesite, which are indicative of a transformation into secondary mineral phases, were not observed. All soils were strongly contaminated with Pb with minor concentrations of Cu, Ni, Cd, and Zn. Arsenic was rarely detected. The obtained results are indicated that the soils from the shooting range are contaminated with heavy metals and have evidences of different degree of anthropogenic Pb sources. This study is crucial for the evaluation of heavy metal-contaminated soils in shooting ranges and their environmental effect as well as for the establishment of management strategies for the mitigation of environmental risks.

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Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽

10.3390/ani11030865 ◽

2021 ◽

Vol 11 (3) ◽

pp. 865

Author(s):

Lantian Su ◽

Xinxin Liu ◽

Guangyao Jin ◽

Yue Ma ◽

Haoxin Tan ◽

...

Keyword(s):

Microbial Community ◽

Environmental Factors ◽

Microbial Communities ◽

Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Functional Genes ◽

Martes Zibellina ◽

Clear Cutting ◽

Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

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Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

Frontiers in Microbiology ◽

10.3389/fmicb.2016.01170 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 24

Author(s):

Neng Fei Wang ◽

Tao Zhang ◽

Xiao Yang ◽

Shuang Wang ◽

Yong Yu ◽

...

Keyword(s):

Bacterial Community ◽

Lake Sediments ◽

Lake Area ◽

Arctic Lake

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Trends in NDVI and Tundra Community Composition in the Arctic of NE Alaska Between 1984 and 2009

Ecosystems ◽

10.1007/s10021-015-9858-9 ◽

2015 ◽

Vol 18 (4) ◽

pp. 707-719 ◽

Cited By ~ 28

Author(s):

Robert R. Pattison ◽

Janet C. Jorgenson ◽

Martha K. Raynolds ◽

Jeffery M. Welker

Keyword(s):

Community Composition ◽

The Arctic

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Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil

Archaea ◽

10.1155/2015/646820 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 14

Author(s):

Yendi E. Navarro-Noya ◽

César Valenzuela-Encinas ◽

Alonso Sandoval-Yuriar ◽

Norma G. Jiménez-Bueno ◽

Rodolfo Marsch ◽

...

Keyword(s):

Species Richness ◽

Alpha Diversity ◽

Methanogenic Archaea ◽

Archaeal Community ◽

Soil Samples ◽

Alkaline Soil ◽

Alkaline Soils ◽

Phylogenetic Information ◽

Archaeal Communities ◽

Saline Alkaline Soils

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils.Halobiforma,Halostagnicola,Haloterrigena, andNatronomonaswere found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

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Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory

Canadian Journal of Microbiology ◽

10.1139/w2012-097 ◽

2012 ◽

Vol 58 (10) ◽

pp. 1153-1158 ◽

Cited By ~ 7

Author(s):

Peng Xing ◽

Huabing Li ◽

Qing Liu ◽

Jiuwen Zheng

Keyword(s):

Lake Taihu ◽

Archaeal Community ◽

Oxygen Depletion ◽

16S Rrna Genes ◽

Rrna Genes ◽

Polymorphism Analysis ◽

Methanogenic Community ◽

Controlled Systems ◽

Microcystis Blooms ◽

Different Temperatures

We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.

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